No Prime lenses available with AF-S
Not true!!!
Sigma 30mm f1.4 Prime lens with HSM
And sigma now do a 50mm Prime with HSM (bit pricey, but initial reviews are saying its quality is one of the best)
The Nikon 50mm is indeed manual focus, but still meters in all modes on the D40, many people prefer a bit of MF!!
Overall the D40 lens limiting thing is not an issue IMO.
There is a huge amount of Sigma, Nikon and Tamron lenses that now have built in motors, which in general gives you faster auto focusing. I think that you can nearly cover eveything you need with lenses available. Wide angle, prime lenses, up to 300mm with VR
Old lenses will work with manual focus in manual mode.
And I have no intention of upgrading! It takes such great pictures with the right glass in front of it.